SeqAn3 3.4.0-rc.4
The Modern C++ library for sequence analysis.
|
The default traits for seqan3::sam_file_input. More...
#include <seqan3/io/sam_file/input.hpp>
Public Types | |
Member types | |
Definitions to model seqan3::sam_file_input_traits. | |
using | sequence_alphabet = dna5 |
The sequence alphabet is seqan3::dna5. | |
using | sequence_legal_alphabet = dna15 |
The legal sequence alphabet for parsing is seqan3::dna15. | |
template<typename _sequence_alphabet > | |
using | sequence_container = std::vector< _sequence_alphabet > |
The container for a sequence is std::vector. | |
template<typename _id_alphabet > | |
using | id_container = std::basic_string< _id_alphabet > |
The string type for an identifier is std::basic_string. | |
using | quality_alphabet = phred42 |
The alphabet for a quality annotation is seqan3::phred42. | |
template<typename _quality_alphabet > | |
using | quality_container = std::vector< _quality_alphabet > |
The string type for a quality annotation is std::vector. | |
using | ref_sequences = ref_sequences_t |
The type of the reference sequences is deduced on construction. | |
using | ref_ids = ref_ids_t |
The type of the reference identifiers is deduced on construction. | |
Additional Inherited Members | |
![]() | |
using | sequence_alphabet |
Alphabet of the characters for the seqan3::field::seq; must model seqan3::alphabet. | |
using | sequence_legal_alphabet |
Intermediate alphabet for seqan3::field::seq; must model seqan3::alphabet and be convertible to sequence_alphabet . | |
using | sequence_container |
Type template of the seqan3::field::seq, a container template over sequence_alphabet ; must model seqan3::sequence_container. | |
using | id_container |
Type template of the seqan3::field::id, a container template over char ; must model seqan3::sequence_container. | |
using | quality_alphabet |
Alphabet of the characters for the seqan3::field::qual; must model seqan3::writable_quality_alphabet. | |
using | quality_container |
Type template of the seqan3::field::qual, a container template over quality_alphabet ; must model seqan3::sequence_container. | |
using | ref_sequences |
The type of range over reference sequences; must model std::ranges::forward_range, the value_type must also model std::ranges::forward_range, and the value type of the value type must model seqan3::alphabet (e.g. std::vector<std::vector<dna4>>). | |
using | ref_ids |
The type of range over reference sequences; must model std::ranges::forward_range, the value_type must also model std::ranges::forward_range, and the value type of the value type must model seqan3::alphabet (e.g. std::vector<string>). | |
The default traits for seqan3::sam_file_input.
ref_sequences_t | A range over reference sequences. This type is automatically deduced on construction. |
ref_ids_t | A range over reference ids. This type is automatically deduced on construction. |
If you wish to change a single or a few types from the default, just inherit from this class and "overwrite" the respective type definitions.
This example will make the file read into a smaller alphabet and a compressed container: